Multiple sequence alignment - TraesCS5B01G202200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G202200 chr5B 100.000 4524 0 0 1 4524 368484743 368489266 0.000000e+00 8355
1 TraesCS5B01G202200 chr5B 100.000 433 0 0 4891 5323 368489633 368490065 0.000000e+00 800
2 TraesCS5B01G202200 chr5B 74.707 597 135 13 1725 2313 208258255 208258843 8.850000e-63 252
3 TraesCS5B01G202200 chr5D 93.164 3496 129 45 1 3465 318440492 318443908 0.000000e+00 5031
4 TraesCS5B01G202200 chr5D 90.524 1087 52 20 3467 4524 318443962 318445026 0.000000e+00 1389
5 TraesCS5B01G202200 chr5D 89.925 268 11 6 5055 5320 318445299 318445552 1.100000e-86 331
6 TraesCS5B01G202200 chr5D 75.042 597 133 13 1725 2313 204075212 204075800 4.090000e-66 263
7 TraesCS5B01G202200 chr5A 91.806 3283 149 47 283 3508 413040167 413043386 0.000000e+00 4462
8 TraesCS5B01G202200 chr5A 91.088 1066 61 18 3466 4524 413043405 413044443 0.000000e+00 1411
9 TraesCS5B01G202200 chr5A 87.732 269 22 5 5053 5320 413044718 413044976 2.410000e-78 303
10 TraesCS5B01G202200 chr5A 89.316 234 16 6 1 226 413039929 413040161 8.730000e-73 285
11 TraesCS5B01G202200 chr5A 74.372 597 137 14 1725 2313 238694896 238695484 1.920000e-59 241


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G202200 chr5B 368484743 368490065 5322 False 4577.500000 8355 100.000000 1 5323 2 chr5B.!!$F2 5322
1 TraesCS5B01G202200 chr5B 208258255 208258843 588 False 252.000000 252 74.707000 1725 2313 1 chr5B.!!$F1 588
2 TraesCS5B01G202200 chr5D 318440492 318445552 5060 False 2250.333333 5031 91.204333 1 5320 3 chr5D.!!$F2 5319
3 TraesCS5B01G202200 chr5D 204075212 204075800 588 False 263.000000 263 75.042000 1725 2313 1 chr5D.!!$F1 588
4 TraesCS5B01G202200 chr5A 413039929 413044976 5047 False 1615.250000 4462 89.985500 1 5320 4 chr5A.!!$F2 5319
5 TraesCS5B01G202200 chr5A 238694896 238695484 588 False 241.000000 241 74.372000 1725 2313 1 chr5A.!!$F1 588

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
838 900 0.029681 ATAGATCCCACCACAGCCCT 60.030 55.0 0.00 0.0 0.00 5.19 F
1749 1846 1.028330 ACTTCGTCTACATCGGCGGA 61.028 55.0 7.21 0.0 0.00 5.54 F
2406 2503 0.102481 TCAAGGTCGCCGAGCTTATC 59.898 55.0 28.53 0.0 46.62 1.75 F
3905 4069 0.173029 TGGTTGTGTTGCTGCACTTG 59.827 50.0 0.00 0.0 39.89 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2093 1.221840 CGGGGTTGATCACCTCCAG 59.778 63.158 10.16 0.0 44.68 3.86 R
3127 3224 0.249120 CTCGTATCAAGGGCCACACA 59.751 55.000 6.18 0.0 0.00 3.72 R
4058 4222 0.109458 CGAACATGTCCTCGTCGGAA 60.109 55.000 11.03 0.0 45.32 4.30 R
5022 5342 0.179059 TGAGCGAGACCAACAGCAAA 60.179 50.000 0.00 0.0 0.00 3.68 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.796231 CCGGACGGGCACGAAGAG 62.796 72.222 19.19 2.71 44.60 2.85
67 78 7.688918 AAGAGTTTCTTCATATCCTCAGGAT 57.311 36.000 12.08 12.08 37.97 3.24
68 79 8.789767 AAGAGTTTCTTCATATCCTCAGGATA 57.210 34.615 16.23 16.23 39.48 2.59
94 105 1.576356 GTTTTTGTTGGATTGCGGCA 58.424 45.000 0.00 0.00 0.00 5.69
149 160 2.127270 CGCATGCAACCACGTCAC 60.127 61.111 19.57 0.00 0.00 3.67
185 196 1.748879 GCAGGCAAAGGCACCGATA 60.749 57.895 0.00 0.00 43.71 2.92
219 230 2.036475 CCAGGAAGTCACCATCCGATAG 59.964 54.545 0.00 0.00 40.78 2.08
224 235 5.131142 AGGAAGTCACCATCCGATAGAAAAT 59.869 40.000 0.00 0.00 40.78 1.82
225 236 6.326583 AGGAAGTCACCATCCGATAGAAAATA 59.673 38.462 0.00 0.00 40.78 1.40
226 237 6.990349 GGAAGTCACCATCCGATAGAAAATAA 59.010 38.462 0.00 0.00 39.76 1.40
228 239 8.980481 AAGTCACCATCCGATAGAAAATAAAT 57.020 30.769 0.00 0.00 39.76 1.40
290 311 0.537188 AAGTAGCGTGCATAGCAGGT 59.463 50.000 17.41 6.11 44.79 4.00
316 357 9.849166 TGTAAAATTTCGAATTAAGAATCACCC 57.151 29.630 0.00 0.00 0.00 4.61
317 358 9.849166 GTAAAATTTCGAATTAAGAATCACCCA 57.151 29.630 0.00 0.00 0.00 4.51
318 359 8.986477 AAAATTTCGAATTAAGAATCACCCAG 57.014 30.769 0.00 0.00 0.00 4.45
319 360 5.560966 TTTCGAATTAAGAATCACCCAGC 57.439 39.130 0.00 0.00 0.00 4.85
320 361 4.487714 TCGAATTAAGAATCACCCAGCT 57.512 40.909 0.00 0.00 0.00 4.24
321 362 4.191544 TCGAATTAAGAATCACCCAGCTG 58.808 43.478 6.78 6.78 0.00 4.24
322 363 3.313526 CGAATTAAGAATCACCCAGCTGG 59.686 47.826 26.87 26.87 41.37 4.85
402 445 0.106149 GGAAACCGTGGTGACTGACT 59.894 55.000 0.00 0.00 0.00 3.41
404 447 0.814010 AAACCGTGGTGACTGACTGC 60.814 55.000 0.00 0.00 0.00 4.40
413 456 2.555199 GTGACTGACTGCTCACTTGTT 58.445 47.619 0.00 0.00 34.99 2.83
431 474 3.532896 TCTGTAAGAAAGCCAGCCG 57.467 52.632 0.00 0.00 42.31 5.52
432 475 0.036388 TCTGTAAGAAAGCCAGCCGG 60.036 55.000 0.00 0.00 42.31 6.13
433 476 1.002624 TGTAAGAAAGCCAGCCGGG 60.003 57.895 2.18 0.00 40.85 5.73
434 477 1.749258 GTAAGAAAGCCAGCCGGGG 60.749 63.158 2.18 0.00 37.04 5.73
546 602 3.996363 GGTTTGTCATGAATTCTTTGGCC 59.004 43.478 7.05 0.00 0.00 5.36
608 664 3.053291 TGGACGAAATGCCCGTGC 61.053 61.111 0.00 0.00 46.21 5.34
653 709 8.173130 GCGAAATTCCGATTATATTTAATCCGT 58.827 33.333 9.49 0.00 40.35 4.69
757 815 5.559148 ATCCATTCCATTCCAGTCTAGTC 57.441 43.478 0.00 0.00 0.00 2.59
760 818 5.598830 TCCATTCCATTCCAGTCTAGTCTAC 59.401 44.000 0.00 0.00 0.00 2.59
762 820 6.239176 CCATTCCATTCCAGTCTAGTCTACTC 60.239 46.154 0.00 0.00 0.00 2.59
763 821 4.794334 TCCATTCCAGTCTAGTCTACTCC 58.206 47.826 0.00 0.00 0.00 3.85
765 823 4.582656 CCATTCCAGTCTAGTCTACTCCAG 59.417 50.000 0.00 0.00 0.00 3.86
815 877 5.178061 TCCGTTACTTGTAGTCGTGATAGA 58.822 41.667 0.00 0.00 0.00 1.98
816 878 5.819379 TCCGTTACTTGTAGTCGTGATAGAT 59.181 40.000 0.00 0.00 0.00 1.98
817 879 6.986231 TCCGTTACTTGTAGTCGTGATAGATA 59.014 38.462 0.00 0.00 0.00 1.98
818 880 7.170489 TCCGTTACTTGTAGTCGTGATAGATAG 59.830 40.741 0.00 0.00 0.00 2.08
831 893 6.069615 TCGTGATAGATAGATAGATCCCACCA 60.070 42.308 0.00 0.00 0.00 4.17
833 895 6.892456 GTGATAGATAGATAGATCCCACCACA 59.108 42.308 0.00 0.00 0.00 4.17
838 900 0.029681 ATAGATCCCACCACAGCCCT 60.030 55.000 0.00 0.00 0.00 5.19
854 921 1.490574 CCCTTCCGATCCTCAAGAGT 58.509 55.000 0.00 0.00 0.00 3.24
881 948 4.175489 ACGCCGACCGACGATCAG 62.175 66.667 4.99 0.00 45.77 2.90
947 1021 3.564027 CCGTCTTCGCCAATCCGC 61.564 66.667 0.00 0.00 35.54 5.54
983 1057 1.760479 TTCCGCCACCCTCTTTCGAA 61.760 55.000 0.00 0.00 0.00 3.71
984 1059 1.302192 CCGCCACCCTCTTTCGAAA 60.302 57.895 10.71 10.71 0.00 3.46
1068 1143 1.141881 GATCTGTCGATGTGGCGGT 59.858 57.895 0.00 0.00 0.00 5.68
1253 1339 1.134068 CCCGGATTTCTTCTTCCCCTC 60.134 57.143 0.73 0.00 0.00 4.30
1351 1448 4.293415 GAGTTCTTGCTGATTTGTTGGTG 58.707 43.478 0.00 0.00 0.00 4.17
1402 1499 2.241430 TCGAGATCCTACTCCAACCTCA 59.759 50.000 0.00 0.00 33.83 3.86
1567 1664 3.000819 TGGCCTCCGACGACCAAT 61.001 61.111 3.32 0.00 0.00 3.16
1695 1792 2.359107 CTGCGGCAGCTCAAGGAA 60.359 61.111 18.16 0.00 45.42 3.36
1696 1793 1.968017 CTGCGGCAGCTCAAGGAAA 60.968 57.895 18.16 0.00 45.42 3.13
1697 1794 1.919956 CTGCGGCAGCTCAAGGAAAG 61.920 60.000 18.16 0.00 45.42 2.62
1698 1795 2.873288 CGGCAGCTCAAGGAAAGC 59.127 61.111 0.00 0.00 40.14 3.51
1749 1846 1.028330 ACTTCGTCTACATCGGCGGA 61.028 55.000 7.21 0.00 0.00 5.54
1776 1873 2.501610 GACATCCCGGCAGAGGAC 59.498 66.667 0.00 0.00 35.85 3.85
2280 2377 1.392710 AATACGAGTCGCAGAGGGGG 61.393 60.000 13.59 0.00 36.95 5.40
2347 2444 1.106944 GCCGGTGGGGATACATTTGG 61.107 60.000 1.90 0.00 38.47 3.28
2348 2445 0.467290 CCGGTGGGGATACATTTGGG 60.467 60.000 0.00 0.00 38.47 4.12
2360 2457 3.228243 ATTTGGGGCAGCTGCAGGA 62.228 57.895 37.63 18.88 44.36 3.86
2361 2458 3.873679 TTTGGGGCAGCTGCAGGAG 62.874 63.158 37.63 0.81 44.36 3.69
2406 2503 0.102481 TCAAGGTCGCCGAGCTTATC 59.898 55.000 28.53 0.00 46.62 1.75
2417 2514 2.464865 CGAGCTTATCAAGGAGTTCCG 58.535 52.381 0.00 0.00 42.08 4.30
2454 2551 5.300411 TCATGATGCTTGGTGTAGATGAT 57.700 39.130 0.00 0.00 0.00 2.45
2742 2839 4.560743 TGCTGCTTGGTGACCGCA 62.561 61.111 4.18 4.18 35.01 5.69
2981 3078 1.056700 ACAGGTGAAGGTGAGCAGGT 61.057 55.000 0.00 0.00 0.00 4.00
3126 3223 2.919602 AGGATTTGGGCTAAGGTTCAGA 59.080 45.455 0.00 0.00 0.00 3.27
3127 3224 3.529319 AGGATTTGGGCTAAGGTTCAGAT 59.471 43.478 0.00 0.00 0.00 2.90
3128 3225 3.633986 GGATTTGGGCTAAGGTTCAGATG 59.366 47.826 0.00 0.00 0.00 2.90
3164 3261 4.268687 CTTCAAGAAGCTCGCGGT 57.731 55.556 6.13 0.00 0.00 5.68
3179 3276 0.670546 GCGGTTGAGCAGCTTGTCTA 60.671 55.000 0.00 0.00 35.39 2.59
3180 3277 2.009042 GCGGTTGAGCAGCTTGTCTAT 61.009 52.381 0.00 0.00 35.39 1.98
3240 3337 0.250467 ATGATGGTACGCTGATGCCC 60.250 55.000 0.00 0.00 35.36 5.36
3328 3425 6.813649 CGATGAGAAGAACTTGGTCTTAATCA 59.186 38.462 14.22 14.22 37.98 2.57
3343 3440 5.008613 GTCTTAATCACAAGCACAAAGACCA 59.991 40.000 0.00 0.00 36.81 4.02
3449 3548 5.774498 ACTGTTCCCTGAAAATTCTCAAC 57.226 39.130 0.00 0.00 0.00 3.18
3487 3647 7.847487 TGACATTGTTGAAACGAAACTACTAG 58.153 34.615 0.00 0.00 0.00 2.57
3488 3648 7.493320 TGACATTGTTGAAACGAAACTACTAGT 59.507 33.333 0.00 0.00 0.00 2.57
3490 3650 9.485206 ACATTGTTGAAACGAAACTACTAGTAT 57.515 29.630 2.33 0.00 0.00 2.12
3508 3668 7.091443 ACTAGTATTGCTGTGACTTTGTACTC 58.909 38.462 0.00 0.00 0.00 2.59
3514 3674 3.187227 GCTGTGACTTTGTACTCCACATG 59.813 47.826 0.00 0.00 36.90 3.21
3517 3677 5.538118 TGTGACTTTGTACTCCACATGTAG 58.462 41.667 0.00 0.00 36.90 2.74
3523 3683 2.233676 TGTACTCCACATGTAGCCTGTG 59.766 50.000 0.00 0.00 42.88 3.66
3714 3874 1.004918 GTGGTGCTACAAGGACGCT 60.005 57.895 0.00 0.00 37.44 5.07
3756 3916 1.452833 GGCCAAGGAGCTCCATGAC 60.453 63.158 34.07 25.15 36.89 3.06
3840 4000 2.552743 GGTGAAGCCACAGGTAAAGTTC 59.447 50.000 0.00 0.00 44.93 3.01
3852 4012 2.031420 GGTAAAGTTCGGCTGAAACCAC 60.031 50.000 18.18 10.62 35.46 4.16
3853 4013 2.052782 AAAGTTCGGCTGAAACCACT 57.947 45.000 10.18 0.00 35.46 4.00
3859 4019 2.564721 GGCTGAAACCACTGGTGCC 61.565 63.158 10.69 10.69 35.34 5.01
3870 4030 1.338020 CACTGGTGCCTTTGTTTCCTC 59.662 52.381 0.00 0.00 0.00 3.71
3875 4035 2.224793 GGTGCCTTTGTTTCCTCCTACT 60.225 50.000 0.00 0.00 0.00 2.57
3892 4052 3.830755 CCTACTGTACCTAGTGTGGTTGT 59.169 47.826 0.00 0.00 41.22 3.32
3893 4053 3.746045 ACTGTACCTAGTGTGGTTGTG 57.254 47.619 0.00 0.00 41.22 3.33
3895 4055 3.453353 ACTGTACCTAGTGTGGTTGTGTT 59.547 43.478 0.00 0.00 41.22 3.32
3896 4056 3.799366 TGTACCTAGTGTGGTTGTGTTG 58.201 45.455 0.00 0.00 41.22 3.33
3905 4069 0.173029 TGGTTGTGTTGCTGCACTTG 59.827 50.000 0.00 0.00 39.89 3.16
3911 4075 2.159448 TGTGTTGCTGCACTTGTGTAAC 60.159 45.455 0.00 0.00 39.89 2.50
3912 4076 1.403679 TGTTGCTGCACTTGTGTAACC 59.596 47.619 0.00 0.00 34.36 2.85
3916 4080 1.069906 GCTGCACTTGTGTAACCGAAG 60.070 52.381 0.00 0.00 34.36 3.79
3942 4106 4.025015 GCACTAAGCCATGAGAATGTTG 57.975 45.455 0.00 0.00 37.23 3.33
3943 4107 3.441572 GCACTAAGCCATGAGAATGTTGT 59.558 43.478 0.00 0.00 37.23 3.32
3944 4108 4.082571 GCACTAAGCCATGAGAATGTTGTT 60.083 41.667 0.00 0.00 37.23 2.83
3945 4109 5.565439 GCACTAAGCCATGAGAATGTTGTTT 60.565 40.000 0.00 0.00 37.23 2.83
3946 4110 5.860182 CACTAAGCCATGAGAATGTTGTTTG 59.140 40.000 0.00 0.00 0.00 2.93
3947 4111 3.308438 AGCCATGAGAATGTTGTTTGC 57.692 42.857 0.00 0.00 0.00 3.68
3948 4112 2.629137 AGCCATGAGAATGTTGTTTGCA 59.371 40.909 0.00 0.00 0.00 4.08
3949 4113 3.259876 AGCCATGAGAATGTTGTTTGCAT 59.740 39.130 0.00 0.00 0.00 3.96
3950 4114 3.369756 GCCATGAGAATGTTGTTTGCATG 59.630 43.478 0.00 0.00 33.38 4.06
3951 4115 4.811908 CCATGAGAATGTTGTTTGCATGA 58.188 39.130 0.00 0.00 35.02 3.07
3977 4141 2.839098 CAGGGTGTGAGCAAGGGT 59.161 61.111 0.00 0.00 0.00 4.34
4121 4285 4.798682 CCCTACCTGAGCCCCGGT 62.799 72.222 0.00 0.00 37.31 5.28
4317 4499 3.680786 CCGACGACACCTGGCTGA 61.681 66.667 0.00 0.00 0.00 4.26
4389 4572 5.709164 GCCTGAATAAGACAGCATAATGGAT 59.291 40.000 0.00 0.00 34.47 3.41
4390 4573 6.349115 GCCTGAATAAGACAGCATAATGGATG 60.349 42.308 0.00 0.00 38.73 3.51
4391 4574 6.150641 CCTGAATAAGACAGCATAATGGATGG 59.849 42.308 0.00 0.00 35.91 3.51
4392 4575 6.840527 TGAATAAGACAGCATAATGGATGGA 58.159 36.000 0.00 0.00 35.91 3.41
4418 4601 2.159181 GTCGTAAACGGCAGCATGT 58.841 52.632 1.62 0.00 44.43 3.21
4420 4603 0.515127 TCGTAAACGGCAGCATGTTG 59.485 50.000 5.00 5.00 40.29 3.33
4421 4604 0.237235 CGTAAACGGCAGCATGTTGT 59.763 50.000 11.44 0.00 39.31 3.32
4422 4605 1.685302 GTAAACGGCAGCATGTTGTG 58.315 50.000 11.44 6.87 39.31 3.33
4426 4611 1.081242 CGGCAGCATGTTGTGTTCC 60.081 57.895 11.44 2.88 39.31 3.62
4495 4682 5.148568 CGTTGAACTTGGTTAAATTACCGG 58.851 41.667 0.00 0.00 41.28 5.28
4512 4699 2.823747 ACCGGCTAAAAATTTCCAGACC 59.176 45.455 0.00 0.00 0.00 3.85
4513 4700 2.823154 CCGGCTAAAAATTTCCAGACCA 59.177 45.455 0.00 0.00 0.00 4.02
4514 4701 3.447229 CCGGCTAAAAATTTCCAGACCAT 59.553 43.478 0.00 0.00 0.00 3.55
4515 4702 4.440112 CCGGCTAAAAATTTCCAGACCATC 60.440 45.833 0.00 0.00 0.00 3.51
4516 4703 4.399303 CGGCTAAAAATTTCCAGACCATCT 59.601 41.667 0.00 0.00 0.00 2.90
4517 4704 5.588648 CGGCTAAAAATTTCCAGACCATCTA 59.411 40.000 0.00 0.00 0.00 1.98
4518 4705 6.458342 CGGCTAAAAATTTCCAGACCATCTAC 60.458 42.308 0.00 0.00 0.00 2.59
4519 4706 6.183360 GGCTAAAAATTTCCAGACCATCTACC 60.183 42.308 0.00 0.00 0.00 3.18
4520 4707 6.183360 GCTAAAAATTTCCAGACCATCTACCC 60.183 42.308 0.00 0.00 0.00 3.69
4521 4708 3.560636 AATTTCCAGACCATCTACCCG 57.439 47.619 0.00 0.00 0.00 5.28
4522 4709 0.539986 TTTCCAGACCATCTACCCGC 59.460 55.000 0.00 0.00 0.00 6.13
4523 4710 0.325296 TTCCAGACCATCTACCCGCT 60.325 55.000 0.00 0.00 0.00 5.52
4909 5096 2.467566 TCTACCCGCTGTTTTCCTTC 57.532 50.000 0.00 0.00 0.00 3.46
4910 5097 1.076332 CTACCCGCTGTTTTCCTTCG 58.924 55.000 0.00 0.00 0.00 3.79
4918 5105 3.578688 GCTGTTTTCCTTCGATTTGCAT 58.421 40.909 0.00 0.00 0.00 3.96
4919 5106 3.365820 GCTGTTTTCCTTCGATTTGCATG 59.634 43.478 0.00 0.00 0.00 4.06
4922 5109 4.744137 TGTTTTCCTTCGATTTGCATGTTG 59.256 37.500 0.00 0.00 0.00 3.33
4927 5114 3.120923 CCTTCGATTTGCATGTTGTTTGC 60.121 43.478 0.00 0.00 40.55 3.68
4929 5116 3.051327 TCGATTTGCATGTTGTTTGCTG 58.949 40.909 0.00 0.00 40.77 4.41
4934 5121 2.538437 TGCATGTTGTTTGCTGTTGTC 58.462 42.857 0.00 0.00 40.77 3.18
4973 5185 1.111277 GGGTGTTTGCTGTTGGTCTT 58.889 50.000 0.00 0.00 0.00 3.01
4974 5186 1.480545 GGGTGTTTGCTGTTGGTCTTT 59.519 47.619 0.00 0.00 0.00 2.52
4975 5187 2.093711 GGGTGTTTGCTGTTGGTCTTTT 60.094 45.455 0.00 0.00 0.00 2.27
4976 5188 3.595173 GGTGTTTGCTGTTGGTCTTTTT 58.405 40.909 0.00 0.00 0.00 1.94
4977 5189 3.616821 GGTGTTTGCTGTTGGTCTTTTTC 59.383 43.478 0.00 0.00 0.00 2.29
4978 5190 4.494484 GTGTTTGCTGTTGGTCTTTTTCT 58.506 39.130 0.00 0.00 0.00 2.52
4980 5192 5.408299 GTGTTTGCTGTTGGTCTTTTTCTTT 59.592 36.000 0.00 0.00 0.00 2.52
4981 5193 5.994668 TGTTTGCTGTTGGTCTTTTTCTTTT 59.005 32.000 0.00 0.00 0.00 2.27
4982 5194 6.484977 TGTTTGCTGTTGGTCTTTTTCTTTTT 59.515 30.769 0.00 0.00 0.00 1.94
4983 5195 6.479095 TTGCTGTTGGTCTTTTTCTTTTTG 57.521 33.333 0.00 0.00 0.00 2.44
4984 5196 4.391523 TGCTGTTGGTCTTTTTCTTTTTGC 59.608 37.500 0.00 0.00 0.00 3.68
4985 5197 4.492409 GCTGTTGGTCTTTTTCTTTTTGCG 60.492 41.667 0.00 0.00 0.00 4.85
4986 5198 3.929610 TGTTGGTCTTTTTCTTTTTGCGG 59.070 39.130 0.00 0.00 0.00 5.69
4988 5200 2.159028 TGGTCTTTTTCTTTTTGCGGGG 60.159 45.455 0.00 0.00 0.00 5.73
4990 5202 2.863740 GTCTTTTTCTTTTTGCGGGGTG 59.136 45.455 0.00 0.00 0.00 4.61
4991 5203 2.498078 TCTTTTTCTTTTTGCGGGGTGT 59.502 40.909 0.00 0.00 0.00 4.16
4992 5204 3.055747 TCTTTTTCTTTTTGCGGGGTGTT 60.056 39.130 0.00 0.00 0.00 3.32
4994 5206 2.301577 TTCTTTTTGCGGGGTGTTTG 57.698 45.000 0.00 0.00 0.00 2.93
4995 5207 0.179097 TCTTTTTGCGGGGTGTTTGC 60.179 50.000 0.00 0.00 0.00 3.68
4996 5208 0.179086 CTTTTTGCGGGGTGTTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
4997 5209 0.460987 TTTTTGCGGGGTGTTTGCTG 60.461 50.000 0.00 0.00 0.00 4.41
4998 5210 1.608717 TTTTGCGGGGTGTTTGCTGT 61.609 50.000 0.00 0.00 0.00 4.40
4999 5211 1.608717 TTTGCGGGGTGTTTGCTGTT 61.609 50.000 0.00 0.00 0.00 3.16
5002 5214 2.124693 CGGGGTGTTTGCTGTTGGT 61.125 57.895 0.00 0.00 0.00 3.67
5003 5215 1.739667 GGGGTGTTTGCTGTTGGTC 59.260 57.895 0.00 0.00 0.00 4.02
5004 5216 1.739667 GGGTGTTTGCTGTTGGTCC 59.260 57.895 0.00 0.00 0.00 4.46
5005 5217 0.755327 GGGTGTTTGCTGTTGGTCCT 60.755 55.000 0.00 0.00 0.00 3.85
5006 5218 1.111277 GGTGTTTGCTGTTGGTCCTT 58.889 50.000 0.00 0.00 0.00 3.36
5007 5219 1.067060 GGTGTTTGCTGTTGGTCCTTC 59.933 52.381 0.00 0.00 0.00 3.46
5009 5329 2.427095 GTGTTTGCTGTTGGTCCTTCTT 59.573 45.455 0.00 0.00 0.00 2.52
5028 5348 2.021355 TTTTTGCTGGGTGTTTGCTG 57.979 45.000 0.00 0.00 0.00 4.41
5032 5352 1.067916 GCTGGGTGTTTGCTGTTGG 59.932 57.895 0.00 0.00 0.00 3.77
5037 5357 0.307760 GGTGTTTGCTGTTGGTCTCG 59.692 55.000 0.00 0.00 0.00 4.04
5042 5362 0.601046 TTGCTGTTGGTCTCGCTCAG 60.601 55.000 0.00 0.00 0.00 3.35
5043 5363 2.386660 GCTGTTGGTCTCGCTCAGC 61.387 63.158 0.00 0.00 43.12 4.26
5044 5364 1.739562 CTGTTGGTCTCGCTCAGCC 60.740 63.158 0.00 0.00 0.00 4.85
5045 5365 2.811317 GTTGGTCTCGCTCAGCCG 60.811 66.667 0.00 0.00 0.00 5.52
5046 5366 4.069232 TTGGTCTCGCTCAGCCGG 62.069 66.667 0.00 0.00 0.00 6.13
5049 5369 3.749064 GTCTCGCTCAGCCGGTGA 61.749 66.667 1.90 4.87 0.00 4.02
5050 5370 3.749064 TCTCGCTCAGCCGGTGAC 61.749 66.667 1.90 0.73 0.00 3.67
5072 5415 2.191680 TGGAGGCGCCAATGATTTG 58.808 52.632 31.54 0.00 45.87 2.32
5152 5497 2.506438 GTCCGTCCGTAGTGCTGC 60.506 66.667 0.00 0.00 0.00 5.25
5211 5556 3.402628 AGTAGGTGTTGCTACTGTTGG 57.597 47.619 0.00 0.00 35.34 3.77
5261 5606 2.941025 CACTGGTGGGGGTGGGAT 60.941 66.667 0.00 0.00 0.00 3.85
5263 5608 3.743017 CTGGTGGGGGTGGGATGG 61.743 72.222 0.00 0.00 0.00 3.51
5265 5610 3.420482 GGTGGGGGTGGGATGGAG 61.420 72.222 0.00 0.00 0.00 3.86
5266 5611 3.420482 GTGGGGGTGGGATGGAGG 61.420 72.222 0.00 0.00 0.00 4.30
5267 5612 3.967024 TGGGGGTGGGATGGAGGT 61.967 66.667 0.00 0.00 0.00 3.85
5312 5657 3.141083 TGCCATATGGGGTAATAAAGGCA 59.859 43.478 23.30 7.35 41.31 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.864686 CGTCCGGCCTGCGAATTG 61.865 66.667 0.00 0.00 0.00 2.32
67 78 2.642154 TCCAACAAAAACGGCCTCTA 57.358 45.000 0.00 0.00 0.00 2.43
68 79 1.995376 ATCCAACAAAAACGGCCTCT 58.005 45.000 0.00 0.00 0.00 3.69
149 160 4.321899 GCCTGCTGTCAGAAGGATAGATAG 60.322 50.000 28.96 1.80 44.42 2.08
194 205 1.204146 GATGGTGACTTCCTGGCCTA 58.796 55.000 3.32 0.00 0.00 3.93
276 293 1.083489 TTTACACCTGCTATGCACGC 58.917 50.000 2.99 2.99 33.79 5.34
277 294 4.355543 AATTTTACACCTGCTATGCACG 57.644 40.909 0.00 0.00 33.79 5.34
278 295 4.793216 CGAAATTTTACACCTGCTATGCAC 59.207 41.667 0.00 0.00 33.79 4.57
279 296 4.697828 TCGAAATTTTACACCTGCTATGCA 59.302 37.500 0.00 0.00 36.92 3.96
280 297 5.229921 TCGAAATTTTACACCTGCTATGC 57.770 39.130 0.00 0.00 0.00 3.14
281 298 9.781834 TTAATTCGAAATTTTACACCTGCTATG 57.218 29.630 0.00 0.00 0.00 2.23
285 302 8.736751 TTCTTAATTCGAAATTTTACACCTGC 57.263 30.769 0.00 0.00 0.00 4.85
290 311 9.849166 GGGTGATTCTTAATTCGAAATTTTACA 57.151 29.630 0.00 0.00 0.00 2.41
327 368 2.093973 TGCTTTGCTTTCGGGACAAAAA 60.094 40.909 0.00 0.00 0.00 1.94
328 369 1.478510 TGCTTTGCTTTCGGGACAAAA 59.521 42.857 0.00 0.00 0.00 2.44
329 370 1.066908 CTGCTTTGCTTTCGGGACAAA 59.933 47.619 0.00 0.00 0.00 2.83
330 371 0.667993 CTGCTTTGCTTTCGGGACAA 59.332 50.000 0.00 0.00 0.00 3.18
331 372 1.795170 GCTGCTTTGCTTTCGGGACA 61.795 55.000 0.00 0.00 0.00 4.02
332 373 1.081175 GCTGCTTTGCTTTCGGGAC 60.081 57.895 0.00 0.00 0.00 4.46
333 374 1.228245 AGCTGCTTTGCTTTCGGGA 60.228 52.632 0.00 0.00 40.93 5.14
334 375 3.359002 AGCTGCTTTGCTTTCGGG 58.641 55.556 0.00 0.00 40.93 5.14
402 445 4.273480 GCTTTCTTACAGAACAAGTGAGCA 59.727 41.667 0.00 0.00 33.26 4.26
404 447 4.816385 TGGCTTTCTTACAGAACAAGTGAG 59.184 41.667 0.00 0.00 33.26 3.51
413 456 0.036388 CCGGCTGGCTTTCTTACAGA 60.036 55.000 0.00 0.00 34.21 3.41
426 469 4.431131 AATGCTCACCCCCGGCTG 62.431 66.667 0.00 0.00 0.00 4.85
427 470 4.431131 CAATGCTCACCCCCGGCT 62.431 66.667 0.00 0.00 0.00 5.52
428 471 3.721370 ATCAATGCTCACCCCCGGC 62.721 63.158 0.00 0.00 0.00 6.13
429 472 1.526917 GATCAATGCTCACCCCCGG 60.527 63.158 0.00 0.00 0.00 5.73
430 473 1.889105 CGATCAATGCTCACCCCCG 60.889 63.158 0.00 0.00 0.00 5.73
431 474 0.533755 CTCGATCAATGCTCACCCCC 60.534 60.000 0.00 0.00 0.00 5.40
432 475 0.179000 ACTCGATCAATGCTCACCCC 59.821 55.000 0.00 0.00 0.00 4.95
433 476 1.293924 CACTCGATCAATGCTCACCC 58.706 55.000 0.00 0.00 0.00 4.61
434 477 1.134699 TCCACTCGATCAATGCTCACC 60.135 52.381 0.00 0.00 0.00 4.02
546 602 2.813908 GCCGTCCACCTAACAGCG 60.814 66.667 0.00 0.00 0.00 5.18
584 640 4.160635 CATTTCGTCCACGGGCGC 62.161 66.667 4.91 0.00 40.29 6.53
585 641 4.160635 GCATTTCGTCCACGGGCG 62.161 66.667 3.04 3.04 40.29 6.13
586 642 3.810896 GGCATTTCGTCCACGGGC 61.811 66.667 0.00 0.00 40.29 6.13
587 643 3.131478 GGGCATTTCGTCCACGGG 61.131 66.667 0.00 0.00 40.18 5.28
598 654 0.466189 CCTGGATAAGCACGGGCATT 60.466 55.000 14.57 5.95 44.61 3.56
608 664 1.871080 CGCTAAGCACCCTGGATAAG 58.129 55.000 0.00 0.00 0.00 1.73
757 815 4.867608 GCTTTTGCTTCTCTACTGGAGTAG 59.132 45.833 7.41 7.41 44.36 2.57
760 818 3.006247 GGCTTTTGCTTCTCTACTGGAG 58.994 50.000 0.00 0.00 46.54 3.86
762 820 3.006247 GAGGCTTTTGCTTCTCTACTGG 58.994 50.000 0.00 0.00 46.44 4.00
773 831 1.598701 AATGGAGGCGAGGCTTTTGC 61.599 55.000 0.00 0.00 46.64 3.68
815 877 3.177228 GGCTGTGGTGGGATCTATCTAT 58.823 50.000 0.00 0.00 0.00 1.98
816 878 2.609747 GGCTGTGGTGGGATCTATCTA 58.390 52.381 0.00 0.00 0.00 1.98
817 879 1.428869 GGCTGTGGTGGGATCTATCT 58.571 55.000 0.00 0.00 0.00 1.98
818 880 0.398318 GGGCTGTGGTGGGATCTATC 59.602 60.000 0.00 0.00 0.00 2.08
831 893 0.909610 TTGAGGATCGGAAGGGCTGT 60.910 55.000 0.00 0.00 38.61 4.40
833 895 0.325671 TCTTGAGGATCGGAAGGGCT 60.326 55.000 0.00 0.00 38.61 5.19
838 900 1.825474 GGTGACTCTTGAGGATCGGAA 59.175 52.381 2.55 0.00 38.61 4.30
895 969 4.966787 GGAAAGGCGGTGGTGGCA 62.967 66.667 0.00 0.00 36.77 4.92
983 1057 4.756135 CCAGCATTAACCAGCAACAAAATT 59.244 37.500 0.00 0.00 0.00 1.82
984 1059 4.202346 ACCAGCATTAACCAGCAACAAAAT 60.202 37.500 0.00 0.00 0.00 1.82
1351 1448 5.593909 TCCTCTCTCAGATGTGATCTTCTTC 59.406 44.000 0.00 0.00 37.58 2.87
1368 1465 0.179004 ATCTCGACGCCATCCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
1749 1846 4.796231 GGGATGTCGTCGCGCAGT 62.796 66.667 8.75 0.00 0.00 4.40
1770 1867 3.074788 GACCTTGTCCTGGTCCTCT 57.925 57.895 1.76 0.00 46.01 3.69
1776 1873 4.379243 AGCGCGACCTTGTCCTGG 62.379 66.667 12.10 0.00 0.00 4.45
1996 2093 1.221840 CGGGGTTGATCACCTCCAG 59.778 63.158 10.16 0.00 44.68 3.86
2100 2197 1.600636 CGGGCTGTGCAGGAAGAAA 60.601 57.895 1.11 0.00 0.00 2.52
2280 2377 5.597182 TCCATAGTACTCCAGTCCAATGTAC 59.403 44.000 0.00 0.00 35.18 2.90
2417 2514 3.832237 ATGATGCGGCCCCGATCAC 62.832 63.158 11.48 0.00 42.83 3.06
2448 2545 7.932134 TGCCCTTAAATATGTCCATATCATCT 58.068 34.615 0.48 0.00 33.13 2.90
2454 2551 7.017551 AGACTGATGCCCTTAAATATGTCCATA 59.982 37.037 0.00 0.00 0.00 2.74
2469 2566 1.831580 AAAGCTTCAGACTGATGCCC 58.168 50.000 29.77 11.99 45.37 5.36
2577 2674 3.118592 CCTGTACCTCCTTCACATCCTTC 60.119 52.174 0.00 0.00 0.00 3.46
2742 2839 2.133520 AGATTCATGCCATCCCTCACT 58.866 47.619 0.00 0.00 0.00 3.41
3126 3223 0.908910 TCGTATCAAGGGCCACACAT 59.091 50.000 6.18 0.00 0.00 3.21
3127 3224 0.249120 CTCGTATCAAGGGCCACACA 59.751 55.000 6.18 0.00 0.00 3.72
3128 3225 1.090052 GCTCGTATCAAGGGCCACAC 61.090 60.000 6.18 0.00 0.00 3.82
3164 3261 1.280133 AGGCATAGACAAGCTGCTCAA 59.720 47.619 1.00 0.00 36.18 3.02
3328 3425 1.109323 GCCCTGGTCTTTGTGCTTGT 61.109 55.000 0.00 0.00 0.00 3.16
3343 3440 1.065418 CCATTCACTTAAGGTCGCCCT 60.065 52.381 7.53 0.00 45.63 5.19
3449 3548 6.969366 TCAACAATGTCAACAATGAAGGTAG 58.031 36.000 5.25 0.00 37.30 3.18
3487 3647 4.994852 TGGAGTACAAAGTCACAGCAATAC 59.005 41.667 0.00 0.00 0.00 1.89
3488 3648 4.994852 GTGGAGTACAAAGTCACAGCAATA 59.005 41.667 0.00 0.00 0.00 1.90
3490 3650 3.202906 GTGGAGTACAAAGTCACAGCAA 58.797 45.455 0.00 0.00 0.00 3.91
3492 3652 2.833794 TGTGGAGTACAAAGTCACAGC 58.166 47.619 0.00 0.00 36.06 4.40
3514 3674 5.018539 TGGAATGTACATACACAGGCTAC 57.981 43.478 9.21 0.00 39.30 3.58
3517 3677 5.835113 AATTGGAATGTACATACACAGGC 57.165 39.130 9.21 0.00 39.30 4.85
3714 3874 2.487762 GCAAGATCCAAAATCACGGTCA 59.512 45.455 0.00 0.00 0.00 4.02
3756 3916 2.281830 GAGGACACTCTCCAGGTGG 58.718 63.158 0.00 0.00 42.46 4.61
3840 4000 2.908073 GCACCAGTGGTTTCAGCCG 61.908 63.158 13.62 0.00 31.02 5.52
3852 4012 0.961753 GGAGGAAACAAAGGCACCAG 59.038 55.000 0.00 0.00 0.00 4.00
3853 4013 0.555769 AGGAGGAAACAAAGGCACCA 59.444 50.000 0.00 0.00 0.00 4.17
3859 4019 5.485209 AGGTACAGTAGGAGGAAACAAAG 57.515 43.478 0.00 0.00 0.00 2.77
3870 4030 3.830755 ACAACCACACTAGGTACAGTAGG 59.169 47.826 0.00 0.00 42.25 3.18
3875 4035 3.799366 CAACACAACCACACTAGGTACA 58.201 45.455 0.00 0.00 42.25 2.90
3892 4052 1.403679 GGTTACACAAGTGCAGCAACA 59.596 47.619 0.00 0.00 0.00 3.33
3893 4053 1.596954 CGGTTACACAAGTGCAGCAAC 60.597 52.381 0.00 0.00 0.00 4.17
3895 4055 0.179070 TCGGTTACACAAGTGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
3896 4056 0.941542 TTCGGTTACACAAGTGCAGC 59.058 50.000 0.00 0.00 0.00 5.25
3905 4069 1.272769 AGTGCTCTCCTTCGGTTACAC 59.727 52.381 0.00 0.00 0.00 2.90
3911 4075 0.179097 GGCTTAGTGCTCTCCTTCGG 60.179 60.000 0.00 0.00 42.39 4.30
3912 4076 0.532573 TGGCTTAGTGCTCTCCTTCG 59.467 55.000 0.00 0.00 42.39 3.79
3916 4080 1.759445 TCTCATGGCTTAGTGCTCTCC 59.241 52.381 0.00 0.00 42.39 3.71
3917 4081 3.533606 TTCTCATGGCTTAGTGCTCTC 57.466 47.619 0.00 0.00 42.39 3.20
3919 4083 3.539604 ACATTCTCATGGCTTAGTGCTC 58.460 45.455 0.00 0.00 42.39 4.26
3920 4084 3.641434 ACATTCTCATGGCTTAGTGCT 57.359 42.857 0.00 0.00 42.39 4.40
3921 4085 3.441572 ACAACATTCTCATGGCTTAGTGC 59.558 43.478 0.00 0.00 41.94 4.40
3947 4111 1.206132 ACACCCTGCAATGCAATCATG 59.794 47.619 9.92 8.02 38.41 3.07
3948 4112 1.206132 CACACCCTGCAATGCAATCAT 59.794 47.619 9.92 0.00 38.41 2.45
3949 4113 0.604073 CACACCCTGCAATGCAATCA 59.396 50.000 9.92 0.00 38.41 2.57
3950 4114 0.889994 TCACACCCTGCAATGCAATC 59.110 50.000 9.92 0.00 38.41 2.67
3951 4115 0.892755 CTCACACCCTGCAATGCAAT 59.107 50.000 9.92 0.00 38.41 3.56
3957 4121 1.529010 CCTTGCTCACACCCTGCAA 60.529 57.895 0.00 0.00 43.25 4.08
3977 4141 3.390521 ATCCGCTTCGCCACCAGA 61.391 61.111 0.00 0.00 0.00 3.86
4035 4199 4.131088 GTCCCCGACGCAGAGGAC 62.131 72.222 8.27 8.27 41.87 3.85
4058 4222 0.109458 CGAACATGTCCTCGTCGGAA 60.109 55.000 11.03 0.00 45.32 4.30
4291 4473 3.533105 TGTCGTCGGTGCTGGTGT 61.533 61.111 0.00 0.00 0.00 4.16
4300 4482 3.220999 TTCAGCCAGGTGTCGTCGG 62.221 63.158 0.00 0.00 0.00 4.79
4340 4522 4.099170 GCGCTGCTGCTGGTCTTG 62.099 66.667 14.03 0.00 36.97 3.02
4413 4596 0.664166 CCAAGCGGAACACAACATGC 60.664 55.000 0.00 0.00 0.00 4.06
4417 4600 0.454196 ACAACCAAGCGGAACACAAC 59.546 50.000 0.00 0.00 35.59 3.32
4418 4601 1.135257 CAACAACCAAGCGGAACACAA 60.135 47.619 0.00 0.00 35.59 3.33
4420 4603 0.454196 ACAACAACCAAGCGGAACAC 59.546 50.000 0.00 0.00 35.59 3.32
4421 4604 1.133407 GAACAACAACCAAGCGGAACA 59.867 47.619 0.00 0.00 35.59 3.18
4422 4605 1.404035 AGAACAACAACCAAGCGGAAC 59.596 47.619 0.00 0.00 35.59 3.62
4426 4611 0.594796 GGCAGAACAACAACCAAGCG 60.595 55.000 0.00 0.00 0.00 4.68
4495 4682 6.183360 GGGTAGATGGTCTGGAAATTTTTAGC 60.183 42.308 0.00 0.00 0.00 3.09
4894 5081 1.165270 AATCGAAGGAAAACAGCGGG 58.835 50.000 0.00 0.00 0.00 6.13
4905 5092 3.120923 GCAAACAACATGCAAATCGAAGG 60.121 43.478 0.00 0.00 43.29 3.46
4906 5093 3.737266 AGCAAACAACATGCAAATCGAAG 59.263 39.130 0.00 0.00 46.22 3.79
4907 5094 3.490155 CAGCAAACAACATGCAAATCGAA 59.510 39.130 0.00 0.00 46.22 3.71
4908 5095 3.051327 CAGCAAACAACATGCAAATCGA 58.949 40.909 0.00 0.00 46.22 3.59
4909 5096 2.796031 ACAGCAAACAACATGCAAATCG 59.204 40.909 0.00 0.00 46.22 3.34
4910 5097 4.034279 ACAACAGCAAACAACATGCAAATC 59.966 37.500 0.00 0.00 46.22 2.17
4946 5133 0.460987 CAGCAAACACCCCGCAAAAA 60.461 50.000 0.00 0.00 0.00 1.94
4948 5135 1.608717 AACAGCAAACACCCCGCAAA 61.609 50.000 0.00 0.00 0.00 3.68
4949 5136 2.055042 AACAGCAAACACCCCGCAA 61.055 52.632 0.00 0.00 0.00 4.85
4950 5137 2.441164 AACAGCAAACACCCCGCA 60.441 55.556 0.00 0.00 0.00 5.69
4951 5138 2.027460 CAACAGCAAACACCCCGC 59.973 61.111 0.00 0.00 0.00 6.13
4952 5139 2.070654 GACCAACAGCAAACACCCCG 62.071 60.000 0.00 0.00 0.00 5.73
4953 5140 0.755327 AGACCAACAGCAAACACCCC 60.755 55.000 0.00 0.00 0.00 4.95
4954 5141 1.111277 AAGACCAACAGCAAACACCC 58.889 50.000 0.00 0.00 0.00 4.61
4955 5142 2.959507 AAAGACCAACAGCAAACACC 57.040 45.000 0.00 0.00 0.00 4.16
4956 5143 4.494484 AGAAAAAGACCAACAGCAAACAC 58.506 39.130 0.00 0.00 0.00 3.32
4958 5145 6.480524 AAAAGAAAAAGACCAACAGCAAAC 57.519 33.333 0.00 0.00 0.00 2.93
4973 5185 3.003480 CAAACACCCCGCAAAAAGAAAA 58.997 40.909 0.00 0.00 0.00 2.29
4974 5186 2.622436 CAAACACCCCGCAAAAAGAAA 58.378 42.857 0.00 0.00 0.00 2.52
4975 5187 1.740718 GCAAACACCCCGCAAAAAGAA 60.741 47.619 0.00 0.00 0.00 2.52
4976 5188 0.179097 GCAAACACCCCGCAAAAAGA 60.179 50.000 0.00 0.00 0.00 2.52
4977 5189 0.179086 AGCAAACACCCCGCAAAAAG 60.179 50.000 0.00 0.00 0.00 2.27
4978 5190 0.460987 CAGCAAACACCCCGCAAAAA 60.461 50.000 0.00 0.00 0.00 1.94
4980 5192 1.608717 AACAGCAAACACCCCGCAAA 61.609 50.000 0.00 0.00 0.00 3.68
4981 5193 2.055042 AACAGCAAACACCCCGCAA 61.055 52.632 0.00 0.00 0.00 4.85
4982 5194 2.441164 AACAGCAAACACCCCGCA 60.441 55.556 0.00 0.00 0.00 5.69
4983 5195 2.027460 CAACAGCAAACACCCCGC 59.973 61.111 0.00 0.00 0.00 6.13
4984 5196 2.070654 GACCAACAGCAAACACCCCG 62.071 60.000 0.00 0.00 0.00 5.73
4985 5197 1.739667 GACCAACAGCAAACACCCC 59.260 57.895 0.00 0.00 0.00 4.95
4986 5198 0.755327 AGGACCAACAGCAAACACCC 60.755 55.000 0.00 0.00 0.00 4.61
4988 5200 2.024414 AGAAGGACCAACAGCAAACAC 58.976 47.619 0.00 0.00 0.00 3.32
4990 5202 3.801114 AAAGAAGGACCAACAGCAAAC 57.199 42.857 0.00 0.00 0.00 2.93
4991 5203 4.817318 AAAAAGAAGGACCAACAGCAAA 57.183 36.364 0.00 0.00 0.00 3.68
5009 5329 1.277557 ACAGCAAACACCCAGCAAAAA 59.722 42.857 0.00 0.00 0.00 1.94
5014 5334 1.067916 CCAACAGCAAACACCCAGC 59.932 57.895 0.00 0.00 0.00 4.85
5015 5335 0.385390 GACCAACAGCAAACACCCAG 59.615 55.000 0.00 0.00 0.00 4.45
5017 5337 0.668535 GAGACCAACAGCAAACACCC 59.331 55.000 0.00 0.00 0.00 4.61
5018 5338 0.307760 CGAGACCAACAGCAAACACC 59.692 55.000 0.00 0.00 0.00 4.16
5019 5339 0.317020 GCGAGACCAACAGCAAACAC 60.317 55.000 0.00 0.00 0.00 3.32
5021 5341 0.235926 GAGCGAGACCAACAGCAAAC 59.764 55.000 0.00 0.00 0.00 2.93
5022 5342 0.179059 TGAGCGAGACCAACAGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
5026 5346 1.739562 GGCTGAGCGAGACCAACAG 60.740 63.158 0.00 0.00 0.00 3.16
5028 5348 2.811317 CGGCTGAGCGAGACCAAC 60.811 66.667 0.00 0.00 0.00 3.77
5032 5352 3.749064 TCACCGGCTGAGCGAGAC 61.749 66.667 0.00 0.00 0.00 3.36
5037 5357 4.008933 ACTGGTCACCGGCTGAGC 62.009 66.667 21.69 21.69 46.12 4.26
5042 5362 4.394712 CCTCCACTGGTCACCGGC 62.395 72.222 1.07 0.00 32.02 6.13
5043 5363 4.394712 GCCTCCACTGGTCACCGG 62.395 72.222 0.00 0.00 35.68 5.28
5044 5364 4.742201 CGCCTCCACTGGTCACCG 62.742 72.222 0.00 0.00 0.00 4.94
5049 5369 3.650950 ATTGGCGCCTCCACTGGT 61.651 61.111 29.70 1.21 46.55 4.00
5050 5370 2.898920 ATCATTGGCGCCTCCACTGG 62.899 60.000 29.70 10.06 46.55 4.00
5084 5427 2.896443 GAGCCGAACCAGAGGAGG 59.104 66.667 0.00 0.00 0.00 4.30
5085 5428 2.344203 ACGAGCCGAACCAGAGGAG 61.344 63.158 1.50 0.00 0.00 3.69
5087 5430 2.125912 CACGAGCCGAACCAGAGG 60.126 66.667 1.50 0.00 0.00 3.69
5152 5497 4.596585 AAACCCCACACCAGCCGG 62.597 66.667 0.00 0.00 38.77 6.13
5154 5499 2.983592 CGAAACCCCACACCAGCC 60.984 66.667 0.00 0.00 0.00 4.85
5156 5501 0.616371 TATCCGAAACCCCACACCAG 59.384 55.000 0.00 0.00 0.00 4.00
5158 5503 1.279846 TCTTATCCGAAACCCCACACC 59.720 52.381 0.00 0.00 0.00 4.16
5211 5556 2.213499 CATCATTTGCCGGGAGACTAC 58.787 52.381 2.18 0.00 0.00 2.73
5261 5606 1.618888 GCACCTGACCTACTACCTCCA 60.619 57.143 0.00 0.00 0.00 3.86
5263 5608 1.751924 CAGCACCTGACCTACTACCTC 59.248 57.143 0.00 0.00 32.44 3.85
5265 5610 0.824759 CCAGCACCTGACCTACTACC 59.175 60.000 0.00 0.00 32.44 3.18
5266 5611 1.477295 GACCAGCACCTGACCTACTAC 59.523 57.143 0.00 0.00 32.44 2.73
5267 5612 1.358103 AGACCAGCACCTGACCTACTA 59.642 52.381 0.00 0.00 32.44 1.82


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.